Drop old

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key 0B08240A96F66571)

4 files changed, 6 insertions, 133 deletions

diff --git a/sci-biology/vcftools/ChangeLog b/sci-biology/vcftools/ChangeLog
index cfc9dd1b0653..a895db4e0334 100644
--- a/sci-biology/vcftools/ChangeLog
+++ b/sci-biology/vcftools/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/vcftools
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/ChangeLog,v 1.7 2015/04/03 15:31:25 dilfridge Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/ChangeLog,v 1.8 2015/04/03 19:13:42 dilfridge Exp $
+
+  03 Apr 2015; Andreas K. Huettel <dilfridge@gentoo.org>
+  -vcftools-0.1.7.ebuild, -vcftools-0.1.8.ebuild,
+  -files/vcftools-0.1.8-buildsystem.patch:
+  Drop old
 
 *vcftools-0.1.12b (03 Apr 2015)
 
diff --git a/sci-biology/vcftools/files/vcftools-0.1.8-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.8-buildsystem.patch
deleted file mode 100644
index d8b18e57d806..000000000000
--- a/sci-biology/vcftools/files/vcftools-0.1.8-buildsystem.patch
+++ /dev/null
@@ -1,50 +0,0 @@
- cpp/Makefile |   16 +++++++++++-----
- 1 files changed, 11 insertions(+), 5 deletions(-)
-
-diff --git a/cpp/Makefile b/cpp/Makefile
-index 42d03e4..2f4d4f6 100644
---- a/cpp/Makefile
-+++ b/cpp/Makefile
-@@ -3,7 +3,7 @@
- # ($Revision: 1.2 $)
- 
- # Compiler
--CPP = g++
-+CPP ?= g++
- # Output executable
- EXECUTABLE = vcftools
- # Flag used to turn on compilation of PCA routines
-@@ -11,7 +11,7 @@ ifndef VCFTOOLS_PCA
- 	VCFTOOLS_PCA = 0
- endif
- # Compiler flags
--CPPFLAGS = -O2 -Wall -Wextra
-+CPPFLAGS = -Wall -Wextra
- #CPPFLAGS = -g 
- # Included libraries (zlib)
- LIB = -lz 
-@@ -28,15 +28,21 @@ ifeq ($(VCFTOOLS_PCA), 1)
- 	# Define flag for PCA routine compilation
- 	CPPFLAGS += -DVCFTOOLS_PCA
- 	# Add LAPACK library
--	LIB += -llapack	
-+	LIB += `$(PKG_CONFIG) --libs lapack`
- 	# Add PCA source code
- 	SOURCES += dgeev.cpp
- endif
- 
-+objects := $(patsubst %.cpp,%.o,$(SOURCES))
-+
- all: vcftools
- 
--vcftools: $(SOURCES)
--	$(CPP) $(CPPFLAGS) $(SOURCES) -o $@ $(LIB)
-+vcftools: $(objects)
-+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(objects) -o $@ $(LIB)
-+
-+.cpp.o: $(SOURCES)
-+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) -o $@ $<
-+
- ifdef BINDIR
- 	cp $(CURDIR)/$@ $(BINDIR)/$@
- endif
diff --git a/sci-biology/vcftools/vcftools-0.1.7.ebuild b/sci-biology/vcftools/vcftools-0.1.7.ebuild
deleted file mode 100644
index c5220fae1696..000000000000
--- a/sci-biology/vcftools/vcftools-0.1.7.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/vcftools-0.1.7.ebuild,v 1.1 2012/01/02 21:51:52 weaver Exp $
-
-EAPI=4
-
-MY_P="${PN}_${PV}"
-
-DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
-HOMEPAGE="http://vcftools.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	sed -i -e "s/CPPFLAGS =/CPPFLAGS = $CXXFLAGS /" \
-		-e "s/LIB =/LIB = $LDFLAGS /" cpp/Makefile || die
-}
-
-src_install(){
-	dobin bin/*
-	insinto /usr/share/${PN}/perl
-	doins perl/*.pm
-	exeinto /usr/share/${PN}/perl
-	doexe perl/{fill,vcf}-*
-	echo 'COLON_SEPARATED=PERL5LIB' > "${S}/99${PN}"
-	echo "PERL5LIB=/usr/share/${PN}/perl" >> "${S}/99${PN}"
-	doenvd "${S}/99${PN}"
-	dodoc README.txt
-}
diff --git a/sci-biology/vcftools/vcftools-0.1.8.ebuild b/sci-biology/vcftools/vcftools-0.1.8.ebuild
deleted file mode 100644
index c722ef41ec3b..000000000000
--- a/sci-biology/vcftools/vcftools-0.1.8.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/vcftools-0.1.8.ebuild,v 1.2 2013/02/27 16:39:18 jlec Exp $
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-MY_P="${PN}_${PV}"
-
-DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
-HOMEPAGE="http://vcftools.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="lapack"
-
-RDEPEND="lapack? ( virtual/lapack )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-buildsystem.patch
-	tc-export CXX PKG_CONFIG
-}
-
-src_compile() {
-	local myconf
-	use lapack && myconf="VCFTOOLS_PCA=1"
-	emake -C cpp ${myconf}
-}
-
-src_install(){
-	dobin cpp/${PN}
-	insinto /usr/share/${PN}/perl
-	doins perl/*.pm
-	exeinto /usr/share/${PN}/perl
-	doexe perl/{fill,vcf}-*
-	echo 'COLON_SEPARATED=PERL5LIB' > "${S}/99${PN}"
-	echo "PERL5LIB=/usr/share/${PN}/perl" >> "${S}/99${PN}"
-	doenvd "${S}/99${PN}"
-	dodoc README.txt
-}